FMO DATABASE

FMODB ID: 5Y18Z

Calculation Name: 6HQB-I-Xray547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | (3'r)-3'-hydroxy-beta,beta-caroten-4-one | beta,beta-carotene-4,4'-dione | (1~{s})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(4~{s})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta,beta-caroten-4-one | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | phylloquinone | iron/sulfur cluster | calcium ion | chloride ion

Ligand 3-letter code: CLA | EQ3 | 45D | C7Z | SQD | ECH | BCR | LMG | LHG | LMT | PQN | SF4 | CA | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6HQB

Chain ID: I

ChEMBL ID:

UniProt ID: P29254

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	40
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-133172.868719
FMO2-HF: Nuclear repulsion	117375.414132
FMO2-HF: Total energy	-15797.454587
FMO2-MP2: Total energy	-15841.974043

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-4.553	-5.648	12.284	-4.894	-6.295	-0.013

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.912

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	GLY	0	0.024	0.028	3.847	6.425	7.987	-0.005	-0.546	-1.011	0.000
4	A	4	SER	0	-0.070	-0.054	2.232	-8.901	-11.534	12.252	-4.699	-4.920	-0.013
5	A	5	TYR	0	0.011	0.013	3.422	6.312	6.288	0.037	0.351	-0.364	0.000
6	A	6	ALA	0	0.021	0.007	6.097	-1.198	-1.198	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.019	0.002	8.520	0.067	0.067	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.042	0.020	5.868	2.296	2.296	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.026	0.009	8.019	-0.684	-0.684	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.023	0.015	10.931	1.409	1.409	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.005	-0.008	10.024	1.258	1.258	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.006	0.006	11.492	0.467	0.467	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.039	0.017	13.142	1.081	1.081	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.002	-0.012	15.718	0.922	0.922	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.005	0.014	13.774	0.944	0.944	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.002	-0.007	16.055	1.009	1.009	0.000	0.000	0.000	0.000
17	A	17	MET	0	-0.007	0.017	18.962	0.988	0.988	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.014	-0.021	20.363	0.843	0.843	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.017	-0.002	21.170	0.628	0.628	0.000	0.000	0.000	0.000
20	A	20	TRP	0	-0.030	-0.034	19.771	0.518	0.518	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.008	0.027	25.021	0.537	0.537	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.027	0.010	24.921	0.442	0.442	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.022	0.016	26.215	0.512	0.512	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.028	0.025	29.004	0.409	0.409	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.014	0.003	30.715	0.383	0.383	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.040	-0.027	31.370	0.384	0.384	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.025	-0.015	32.888	0.303	0.303	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.031	0.015	34.882	0.275	0.275	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.010	-0.006	36.495	0.269	0.269	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.034	-0.026	37.334	0.252	0.252	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.011	-0.015	37.222	0.160	0.160	0.000	0.000	0.000	0.000
32	A	32	ILE	0	0.019	0.013	39.512	0.166	0.166	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.038	-0.025	41.782	0.279	0.279	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.071	-0.029	42.967	0.134	0.134	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.988	-0.993	45.136	-6.748	-6.748	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.015	-0.004	46.973	0.159	0.159	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.973	-0.980	49.906	-6.057	-6.057	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.018	-0.011	51.857	0.042	0.042	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-1.005	-0.999	55.703	-5.644	-5.644	0.000	0.000	0.000	0.000
40	A	40	GLY	-1	-1.016	-0.990	58.270	-5.194	-5.194	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)